Advanced Molecular Detection Clips
About Advanced Molecular Detection Clips
Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.
Advanced Molecular Detection Clips Content
NEWS
- FDA approves diagnostic test for chikungunya, dengue, or Zika; CDC to distribute
Outbreak News Today, Mar 19, 2016. - Researchers Sequence Chimpanzee Parasites to Learn About Evolution of Human Malaria Species
Newbern E. GenomeWeb, Mar 22, 2016. - New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data
GenomeWeb, Mar 21, 2016. - Team IDs Potential Gut Microbe Marker for Necrotizing Enterocolitis in Infants
GenomeWeb, Mar 17, 2016. - International Research Team Develops Blood Test for Tuberculosis Risk Assessment
Newbern E. GenomeWeb,Mar 24, 2016.
EVENTS / TRAINING / WEB RESOURCES
- Zika Genome Sequences Available from NCBI
(announcement) NCBI, Mar 17, 2016. - Summer Institute in Statistics and Modeling in Infectious Diseases
(training)Univ of Washington, Seattle. Series of 2.5-day workshops (including molecular epi, contact networks, novel data streams), July 2016. - Submitting Data to NCBI and BioSample
(webinar) NCBI, Apr 13, 1:00-2:00 pm.
CONCEPTS / COMMENTS
- The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson Mark D et al. Scientific data 160018 - An Economic Evaluation of PulseNet: A Network for Foodborne Disease Surveillance.
Scharff Robert L et al. American journal of preventive medicine 2016 Feb
- Translating RNA sequencing into clinical diagnostics: opportunities and challenges.
Byron Sara A et al. Nature reviews. Genetics 2016 Mar - Reimagining the Future of the Diagnosis of Viral Infections.
Peeling Rosanna W et al. The Journal of infectious diseases 2016 Mar
METHODS / TOOLS
- From the desktop to the grid: scalable bioinformatics via workflow conversion.
de la Garza Luis et al. BMC bioinformatics 2016 (1) 127 - Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz M, et al. Nat Methods, Mar 21, 2016. - A method for near full-length amplification and sequencing for six hepatitis C virus genotypes.
Bull Rowena A et al. BMC genomics 2016 (1) 247 - Phylogenetic Analysis of Poliovirus Sequences.
Jorba Jaume et al. Methods in molecular biology (Clifton, N.J.) 2016 227-37 - Flexible data integration and curation using a graph-based approach.
Croset Samuel et al. Bioinformatics (Oxford, England) 2015 Nov
EVOLUTION / ECOLOGY / POPULATIONS
- The genomic signatures of Shigella evolution, adaptation and geographical spread.
The Hao Chung et al. Nature reviews. Microbiology 2016 Apr (4) 235-50 - Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis
Breurec P, et al. bioRxiv, Mar 19, 2016. - Global phylogeography and evolutionary history of Shigella dysenteriae type 1
Njamkepo E, et al. Nat Microbiol, Mar 21, 2016. - Molecular evidence of Burkholderia pseudomallei genotypes based on geographical distribution.
Zulkefli Noorfatin Jihan et al. PeerJ 2016 e1802 - Spatial Temporal Dynamics and Molecular Evolution of Re-Emerging Rabies Virus in Taiwan.
Lin Yung-Cheng et al. International journal of molecular sciences (3) - Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.
de Man Tom J B et al. Genome announcements 2016 (2) - Zika virus in the Americas: Early epidemiological and genetic findings
Faria NR, et al. Science, Mar 24, 2016.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Functional Genome Screening to Elucidate the Colistin Resistance Mechanism.
Kumar Mohit et al. Scientific reports 2016 23156 - Whole genome sequencing provides insights into the genetic determinants of invasiveness in Salmonella Dublin.
Mohammed M et al. Epidemiology and infection 2016 Mar 1-10 - Sensitive sentinel mutation screening reveals differential underestimation of transmitted HIV drug resistance among demographic groups.
Li Jin-Fen et al. AIDS (London, England) 2016 Mar - Detection of chloroquine and artemisinin resistance molecular markers in Plasmodium falciparum: A hospital based study.
Ramani S et al. Tropical parasitology (1) 69-77
DETECTION / DIAGNOSIS
- Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay.
Benitez Alvaro J et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 298-303 - Combined antibody and DNA detection for early diagnosis of leptospirosis after a disaster.
Iwasaki Hiroko et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 287-91 - Discriminative power of Campylobacter phenotypic and genotypic typing methods.
Duarte Alexandra et al. Journal of microbiological methods 2016 Mar - The Impact of Multilocus Variable-Number Tandem-Repeat Analysis on PulseNet Canada Escherichia coli O157:H7 Laboratory Surveillance and Outbreak Support, 2008-2012.
Rumore Jillian Leigh et al. Foodborne pathogens and disease 2016 Mar - Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.
Gyarmati P et al. Scientific reports 23532 - A blood RNA signature for tuberculosis disease risk: a prospective cohort study
Zak DE, et al. Lancet, Mar 23, 2016. - Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR.
Burns Cara C et al. Methods in molecular biology (Clifton, N.J.) 2016 177-212 - Multilocus microsatellite typing of Leishmania infantum isolates in monitored Leishmania/HIV coinfected patients.
Tomás-Pérez Míriam et al. Parasites & vectors 2015 386 - Ribosomal DNA analysis of tsetse and non-tsetse transmitted Ethiopian Trypanosoma vivax strains in view of improved molecular diagnosis.
Fikru Regassa et al. Veterinary parasitology 2016 Apr 15-22
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing.
Yang Shangxin et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 337-42 - A non-autochthonous US strain of Vibrio parahaemolyticus isolated from Chesapeake Bay oysters caused the outbreak in Maryland in 2010.
Haendiges Julie et al. Applied and environmental microbiology 2016 Mar - Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections.
Nickbakhsh S et al. Epidemiology and infection 2016 Mar 1-13 - Human Rabies - Missouri, 2014.
Pratt P Drew et al. MMWR. Morbidity and mortality weekly report 2016 (10) 253-6
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Characterization and complete genome sequence analysis of two Myoviral bacteriophages infecting clinical carbapenem-resistant Acinetobacter baumannii isolates.
Jeon Jongsoo et al. Journal of applied microbiology 2016 Mar - Rapid and long-term immunity elicited by DNA encoded antibody prophylaxis and DNA vaccination against Chikungunya virus.
Muthumani Karuppiah et al. The Journal of infectious diseases 2016 Mar
HOST-MICROBE INTERACTIONS
- Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
Ward DV, et al. Cell Rep, Mar 17, 2016. - Metabolic crosstalk between host and pathogen: sensing, adapting and competing.
Olive Andrew J et al. Nature reviews. Microbiology 2016 Apr (4) 221-34 - The maternal microbiota drives early postnatal innate immune development.
Gomez de Agüero Mercedes et al. Science (New York, N.Y.) 2016 Mar (6279) 1296-302 - Tumour-associated and non-tumour-associated microbiota in colorectal cancer.
Flemer Burkhardt et al. Gut 2016 Mar - Clinical significance of the CCR5delta32 allele in hepatitis C.
Morard Isabelle et al. PloS one 2014 (9) e106424 - Responder Interferon Lambda genotypes are associated with higher risk of liver fibrosis in HIV-Hepatitis C Virus Co-infection.
Moqueet Nasheed et al. The Journal of infectious diseases 2016 Mar
indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.
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